Bit of a backstory. I've been a proud 3G TL (05, 6 speed manual, nav unit) owner for about eight months. The previous owner messed around with he car quite a bit, trying to make it as cool as he could without investing too much money. He replaced all the interior lights with LEDs, added an aux cable (more on that later), illegally tinted the windows, changed the color of the turn signals, added stickers and carbon fiber wrap, removed the resonator, destroyed the trans for me, etc.

A few months ago, I removed the headlights to clean them and replace the HIDs - a lot of you should know that that process involves taking off the front bumper. I didn't want to accidentally set the airbags off, so I disconnected the battery. All in all the battery was disconnected for about four hours. The cleaning/replacement/reinstall went off without a hitch, to the best of my knowledge everything went back exactly how it was before. So I start up the car, put in the codes for the nav and the audio system, and I immediately noticed the XM was working. This struck me as odd, since I had always gone to the XM channel to use the aux cord, my assumption was the XM was disabled and replaced entirely by the aux. Over the next couple weeks, I found more issues that I didn't notice immediately.

Overall, the list of problems that seem to have directly resulted from pulling the bumper and battery are as follows:
- Aux cord appears to be entirely useless, replaced by XM.
- Audio buttons require multiple presses to get a response. For example, to switch from AM/FM to XM, I have to press the button at least twice, sometimes over five times. This applies to touchscreen buttons as well. Doesn't seem to apply to the navigation side of things, only audio features.
- The navigation voice has a tendency to not speak when it should. Sometimes it does just fine, other times I can hear it silence the music as if it's about to speak, but it doesn't say anything.
- Audio system occasionally shuts itself off, or starts when I start the car but remains silent until I restart it.

Also, I have a disconnected HFL unit (it was running the battery down). Not sure if that has anything to do with it. I have no clue what methods were used to install the aux cord or any other electronics, and I'm not in contact with the previous owner to ask. I can see other work that has been done on the car, some of it looks professional, some of it doesn't. The most annoying issue is by far the audio buttons requiring me to hit them more than once, although I'm really missing that aux cord.

I would really appreciate any help, whether it be advice, personal experience, links to similar threads, a straight up fix, etc. I'd bet it has something to do with how the aux cord was installed, but I don't know how to go about fixing it or even finding it. Today I'm trying the classic turn it off and turn it on again (with the battery), but I kind of doubt that will fix it.

 

I've never heard of such issues arising because you disconnected the battery. Also, removing the bumper should have no impact on your internal electronic components whatsoever.
Maybe provide photographs of the aux wire and all other relevant stuff.
I own a 07 and my aux port is located in the middle compartment, so im not sure if the 05 comes that way.
In either case, I would disconnect the battery and connect after a few minutes and see if that has any effect.
In regards to your buttons for audio, do your TL have navigation?